It seems it isn't a problem with the launcher alone. Scenarios also appear twice in the scenario menu.

Hello,
could you please confirm the behavior you observe for me: as Launcher starts it lists all Steam mods twice and after a second the duplicates disappear. Is that right?

I had to go back to stable branch yesterday for community event, and now the issue is gone (I am back on dev yet again) But I can tell you that the issue did not disappeared after a few seconds, I actually needed like half an hour to get the mods properly loaded for the event because some of the duplications refused to become ready.

Hello,
thank you for the reply.

It seems that in the end Launcher was receiving list of subscribed items from Steam with some items duplicated in it and these duplicates were causing all kinds of weird behavior. I've put some filter to Launcher to remove the duplicates and also to remove duplicates from Launcher cache if the duplicate items were already persisted.
The fix should hit the dev-branch on Monday.

Those are great news, looking forward for the patch. Thank you.